Thanks Douglas,
I definitely appreciate your help.
Here is what it Spit out,
*Rémy Wahnoun, PhD*
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
*www.NeuralControl.net http://www.neuralcontrol.net/*
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 11 != 0 )
set flag = $argv[1] ; shift ;
set flag = --n
shift
switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 10 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 1
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 9 != 0 )
set flag = $argv[1] ; shift ;
set flag = --proto-iters
shift
switch ( $flag )
switch ( --proto-iters )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set nProtoIters = $argv[1] ; shift ;
set nProtoIters = 1000
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = --distance
shift
switch ( $flag )
switch ( --distance )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set Distance = $argv[1] ; shift ;
set Distance = 50
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --no-rescale
shift
switch ( $flag )
switch ( --no-rescale )
set DoRescale = 0 ;
set DoRescale = 0
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = orig_nu.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
goto check_params_return ;
goto check_params_return
set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname orig_nu.mgz
mkdir -p $OutDir ;
mkdir -p .
if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/usr/local/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
tee -a ./mri_nu_correct.mni.log
--debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
echo "nIters $nIters" | tee -a $LF
echo nIters 1
tee -a ./mri_nu_correct.mni.log
nIters 1
echo $VERSION | tee -a $LF
tee -a ./mri_nu_correct.mni.log
echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
uname -a | tee -a $LF
uname -a
tee -a ./mri_nu_correct.mni.log
Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux
date | tee -a $LF
date
tee -a ./mri_nu_correct.mni.log
Mon Jun 23 15:32:45 EDT 2014
nu_correct -version | tee -a $LF
nu_correct -version
tee -a ./mri_nu_correct.mni.log
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745
set tmpdir = ./tmp.mri_nu_correct.mni.1745
mkdir -p $tmpdir
mkdir -p ./tmp.mri_nu_correct.mni.1745
echo "tmpdir is $tmpdir" | tee -a $LF
echo tmpdir is ./tmp.mri_nu_correct.mni.1745
tee -a ./mri_nu_correct.mni.log
tmpdir is ./tmp.mri_nu_correct.mni.1745
set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc )
if ( $UseFloat ) set cmd = ( $cmd -odt float )
if ( 1 ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
pwd | & tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
echo $cmd | & tee -a $LF
echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$cmd | & tee -a $LF
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=25.00, TE=5.36, TI=0.00, flip angle=30.00
i_ras = (-1, 1.49012e-08, 0)
j_ras = (0, 0, -1)
k_ras = (-1.30385e-08, 1, -5.96046e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc...
if ( $status ) then
if ( 0 ) then
@ nthIter = 1 ;
@ nthIter = 1
while ( $nthIter < = $nIters )
while ( 1 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo "--------------------------------------------------------" | & tee -a $LF
echo --------------------------------------------------------
tee -a ./mri_nu_correct.mni.log
--------------------------------------------------------
echo "Iteration $nthIter `date`" | & tee -a $LF
echo Iteration 1 `date`
tee -a ./mri_nu_correct.mni.log
date
Iteration 1 Mon Jun 23 15:32:49 EDT 2014
@ m = $nthIter - 1
@ m = 1 - 1
set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc )
set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ;
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ )
if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop )
if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm )
echo $cmd | & tee -a $LF
echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
$cmd | & tee -a $LF
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
[fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] [2014-06-23 15:32:49] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
if ( $status ) then
if ( 0 ) then
rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp
rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu0.imp
@ nthIter = $nthIter + 1 ;
@ nthIter = 1 + 1
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
end
end
while ( $nthIter < = $nIters )
while ( 2 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
set numnc = $tmpdir/nu$nIters.mnc
set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc
if ( $DoRescale ) then
if ( 0 ) then
if ( ! -e $numnc ) then
if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then
echo "ERROR: file $numnc does not exist!" | & tee -a $LF
echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
tee -a ./mri_nu_correct.mni.log
ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
exit 1 ;
exit 1 ------------------------------
This transmission, including any attachments, is for the sole use of the intended recipient (s) and may contain information that is confidential, proprietary, legally privileged, or otherwise protected by law from disclosure. Any unauthorized review, use, copying, disclosure, or distribution is prohibited. If you are not the intended recipient, or the person responsible for delivering this to an addressee, you should notify the sender immediately by telephone or by reply e-mail, and destroy all copies of the original message.
This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz to see if that looks ok
On 06/23/2014 03:58 PM, Remy Wahnoun wrote:
Thanks Douglas,
I definitely appreciate your help.
Here is what it Spit out,
*Rémy Wahnoun, PhD*
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
/www.NeuralControl.net http://www.neuralcontrol.net//
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 11 != 0 )
set flag = $argv[1] ; shift ;
set flag = --n
shift
switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 10 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 1
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 9 != 0 )
set flag = $argv[1] ; shift ;
set flag = --proto-iters
shift
switch ( $flag )
switch ( --proto-iters )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set nProtoIters = $argv[1] ; shift ;
set nProtoIters = 1000
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = --distance
shift
switch ( $flag )
switch ( --distance )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set Distance = $argv[1] ; shift ;
set Distance = 50
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --no-rescale
shift
switch ( $flag )
switch ( --no-rescale )
set DoRescale = 0 ;
set DoRescale = 0
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = orig_nu.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
goto check_params_return ;
goto check_params_return
set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname orig_nu.mgz
mkdir -p $OutDir ;
mkdir -p .
if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/usr/local/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
tee -a ./mri_nu_correct.mni.log
--debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
echo "nIters $nIters" | tee -a $LF
echo nIters 1
tee -a ./mri_nu_correct.mni.log
nIters 1
echo $VERSION | tee -a $LF
tee -a ./mri_nu_correct.mni.log
echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
uname -a | tee -a $LF
uname -a
tee -a ./mri_nu_correct.mni.log
Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux
date | tee -a $LF
date
tee -a ./mri_nu_correct.mni.log
Mon Jun 23 15:32:45 EDT 2014
nu_correct -version | tee -a $LF
nu_correct -version
tee -a ./mri_nu_correct.mni.log
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745
set tmpdir = ./tmp.mri_nu_correct.mni.1745
mkdir -p $tmpdir
mkdir -p ./tmp.mri_nu_correct.mni.1745
echo "tmpdir is $tmpdir" | tee -a $LF
echo tmpdir is ./tmp.mri_nu_correct.mni.1745
tee -a ./mri_nu_correct.mni.log
tmpdir is ./tmp.mri_nu_correct.mni.1745
set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc )
if ( $UseFloat ) set cmd = ( $cmd -odt float )
if ( 1 ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
pwd | & tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
echo $cmd | & tee -a $LF
echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$cmd | & tee -a $LF
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=25.00, TE=5.36, TI=0.00, flip angle=30.00
i_ras = (-1, 1.49012e-08, 0)
j_ras = (0, 0, -1)
k_ras = (-1.30385e-08, 1, -5.96046e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc...
if ( $status ) then
if ( 0 ) then
@ nthIter = 1 ;
@ nthIter = 1
while ( $nthIter < = $nIters )
while ( 1 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo "--------------------------------------------------------" | & tee -a $LF
echo --------------------------------------------------------
tee -a ./mri_nu_correct.mni.log
echo "Iteration $nthIter `date`" | & tee -a $LF
echo Iteration 1 `date`
tee -a ./mri_nu_correct.mni.log
date
Iteration 1 Mon Jun 23 15:32:49 EDT 2014
@ m = $nthIter - 1
@ m = 1 - 1
set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc )
set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ;
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ )
if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop )
if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm )
echo $cmd | & tee -a $LF
echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
$cmd | & tee -a $LF
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
[fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] [2014-06-23 15:32:49] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
if ( $status ) then
if ( 0 ) then
rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp
rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu0.imp
@ nthIter = $nthIter + 1 ;
@ nthIter = 1 + 1
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
end
end
while ( $nthIter < = $nIters )
while ( 2 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
set numnc = $tmpdir/nu$nIters.mnc
set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc
if ( $DoRescale ) then
if ( 0 ) then
if ( ! -e $numnc ) then
if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then
echo "ERROR: file $numnc does not exist!" | & tee -a $LF
echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
tee -a ./mri_nu_correct.mni.log
ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
exit 1 ;
exit 1
This transmission, including any attachments, is for the sole use of the intended recipient (s) and may contain information that is confidential, proprietary, legally privileged, or otherwise protected by law from disclosure. Any unauthorized review, use, copying, disclosure, or distribution is prohibited. If you are not the intended recipient, or the person responsible for delivering this to an addressee, you should notify the sender immediately by telephone or by reply e-mail, and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Douglas, orig.mgz looks fine to me. Do you know if there is any detailed log i could look into? Or maybe process tasks one after the other?
*Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net http://www.NeuralControl.net*
On Wed, Jun 25, 2014 at 7:40 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz to see if that looks ok
On 06/23/2014 03:58 PM, Remy Wahnoun wrote:
Thanks Douglas,
I definitely appreciate your help.
Here is what it Spit out,
*Rémy Wahnoun, PhD*
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
/www.NeuralControl.net http://www.neuralcontrol.net//
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 11 != 0 )
set flag = $argv[1] ; shift ;
set flag = --n
shift
switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 10 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 1
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 9 != 0 )
set flag = $argv[1] ; shift ;
set flag = --proto-iters
shift
switch ( $flag )
switch ( --proto-iters )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set nProtoIters = $argv[1] ; shift ;
set nProtoIters = 1000
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = --distance
shift
switch ( $flag )
switch ( --distance )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set Distance = $argv[1] ; shift ;
set Distance = 50
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --no-rescale
shift
switch ( $flag )
switch ( --no-rescale )
set DoRescale = 0 ;
set DoRescale = 0
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = orig_nu.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
goto check_params_return ;
goto check_params_return
set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname orig_nu.mgz
mkdir -p $OutDir ;
mkdir -p .
if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/usr/local/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
tee -a ./mri_nu_correct.mni.log
--debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
echo "nIters $nIters" | tee -a $LF
echo nIters 1
tee -a ./mri_nu_correct.mni.log
nIters 1
echo $VERSION | tee -a $LF
tee -a ./mri_nu_correct.mni.log
echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
uname -a | tee -a $LF
uname -a
tee -a ./mri_nu_correct.mni.log
Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux
date | tee -a $LF
date
tee -a ./mri_nu_correct.mni.log
Mon Jun 23 15:32:45 EDT 2014
nu_correct -version | tee -a $LF
nu_correct -version
tee -a ./mri_nu_correct.mni.log
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745
set tmpdir = ./tmp.mri_nu_correct.mni.1745
mkdir -p $tmpdir
mkdir -p ./tmp.mri_nu_correct.mni.1745
echo "tmpdir is $tmpdir" | tee -a $LF
echo tmpdir is ./tmp.mri_nu_correct.mni.1745
tee -a ./mri_nu_correct.mni.log
tmpdir is ./tmp.mri_nu_correct.mni.1745
set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc )
if ( $UseFloat ) set cmd = ( $cmd -odt float )
if ( 1 ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
pwd | & tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
echo $cmd | & tee -a $LF
echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt
float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$cmd | & tee -a $LF
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=25.00, TE=5.36, TI=0.00, flip angle=30.00
i_ras = (-1, 1.49012e-08, 0)
j_ras = (0, 0, -1)
k_ras = (-1.30385e-08, 1, -5.96046e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc...
if ( $status ) then
if ( 0 ) then
@ nthIter = 1 ;
@ nthIter = 1
while ( $nthIter < = $nIters )
while ( 1 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo "--------------------------------------------------------" | & tee -a $LF
echo --------------------------------------------------------
tee -a ./mri_nu_correct.mni.log
echo "Iteration $nthIter `date`" | & tee -a $LF
echo Iteration 1 `date`
tee -a ./mri_nu_correct.mni.log
date
Iteration 1 Mon Jun 23 15:32:49 EDT 2014
@ m = $nthIter - 1
@ m = 1 - 1
set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc )
set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ;
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ )
if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop )
if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm )
echo $cmd | & tee -a $LF
echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
$cmd | & tee -a $LF
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
[fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] [2014-06-23 15:32:49] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
if ( $status ) then
if ( 0 ) then
rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp
rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu0.imp
@ nthIter = $nthIter + 1 ;
@ nthIter = 1 + 1
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
end
end
while ( $nthIter < = $nIters )
while ( 2 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
set numnc = $tmpdir/nu$nIters.mnc
set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc
if ( $DoRescale ) then
if ( 0 ) then
if ( ! -e $numnc ) then
if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then
echo "ERROR: file $numnc does not exist!" | & tee -a $LF
echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
tee -a ./mri_nu_correct.mni.log
ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
exit 1 ;
exit 1
This transmission, including any attachments, is for the sole use of the intended recipient (s) and may contain information that is confidential, proprietary, legally privileged, or otherwise protected by law from disclosure. Any unauthorized review, use, copying, disclosure, or distribution is prohibited. If you are not the intended recipient, or the person responsible for delivering this to an addressee, you should notify the sender immediately by telephone or by reply e-mail, and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Can you upload the orig.mgz to me using our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 06/30/2014 03:51 PM, Remy Wahnoun wrote:
Thanks Douglas, orig.mgz looks fine to me. Do you know if there is any detailed log i could look into? Or maybe process tasks one after the other?
*Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University /www.NeuralControl.net http://www.NeuralControl.net/
On Wed, Jun 25, 2014 at 7:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz to see if that looks ok On 06/23/2014 03:58 PM, Remy Wahnoun wrote: > > Thanks Douglas, > > I definitely appreciate your help. > > Here is what it Spit out, > > *Rémy Wahnoun, PhD* > > Biomedical Research Group Manager > > Barrow Neurological Institute at Phoenix Children's Hospital > > Adjunct Faculty, Arizona State University > > /www.NeuralControl.net <http://www.NeuralControl.net> <http://www.neuralcontrol.net/>/ > > set echo = 1 ; > > set debug = 1 ; > > set debug = 1 > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 11 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --n > > shift > > switch ( $flag ) > > switch ( --n ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 10 == 0 ) goto arg1err > > set nIters = $argv[1] ; shift ; > > set nIters = 1 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 9 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --proto-iters > > shift > > switch ( $flag ) > > switch ( --proto-iters ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 8 == 0 ) goto arg1err > > set nProtoIters = $argv[1] ; shift ; > > set nProtoIters = 1000 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 7 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --distance > > shift > > switch ( $flag ) > > switch ( --distance ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 6 == 0 ) goto arg1err > > set Distance = $argv[1] ; shift ; > > set Distance = 50 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 5 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --no-rescale > > shift > > switch ( $flag ) > > switch ( --no-rescale ) > > set DoRescale = 0 ; > > set DoRescale = 0 > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 4 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --i > > shift > > switch ( $flag ) > > switch ( --i ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 3 == 0 ) goto arg1err > > set InVol = $argv[1] ; shift ; > > set InVol = orig.mgz > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 2 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --o > > shift > > switch ( $flag ) > > switch ( --o ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 1 == 0 ) goto arg1err > > set OutVol = $argv[1] ; shift ; > > set OutVol = orig_nu.mgz > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 0 != 0 ) > > goto parse_args_return ; > > goto parse_args_return > > goto check_params ; > > goto check_params > > if ( $#InVol == 0 ) then > > if ( 1 == 0 ) then > > if ( ! -e $InVol ) then > > if ( ! -e orig.mgz ) then > > if ( $#OutVol == 0 ) then > > if ( 1 == 0 ) then > > goto check_params_return ; > > goto check_params_return > > set OutDir = `dirname $OutVol` ; > > set OutDir = `dirname $OutVol` > > dirname orig_nu.mgz > > mkdir -p $OutDir ; > > mkdir -p . > > if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log > > if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log > > set LF = ./mri_nu_correct.mni.log > > if ( -e $LF ) mv $LF $LF.bak > > if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log > ./mri_nu_correct.mni.log.bak > > mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak > > pwd | tee -a $LF > > pwd > > tee -a ./mri_nu_correct.mni.log > > /media/sf_Imagery/FreeSurfer/xx/mri > > which mri_nu_correct.mni | tee -a $LF > > which mri_nu_correct.mni > > tee -a ./mri_nu_correct.mni.log > > /usr/local/freesurfer/bin/mri_nu_correct.mni > > echo $cmdargs | tee -a $LF > > echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i > orig.mgz --o orig_nu.mgz > > tee -a ./mri_nu_correct.mni.log > > --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i > orig.mgz --o orig_nu.mgz > > echo "nIters $nIters" | tee -a $LF > > echo nIters 1 > > tee -a ./mri_nu_correct.mni.log > > nIters 1 > > echo $VERSION | tee -a $LF > > tee -a ./mri_nu_correct.mni.log > > echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > > $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > > uname -a | tee -a $LF > > uname -a > > tee -a ./mri_nu_correct.mni.log > > Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 > 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux > > date | tee -a $LF > > date > > tee -a ./mri_nu_correct.mni.log > > Mon Jun 23 15:32:45 EDT 2014 > > nu_correct -version | tee -a $LF > > nu_correct -version > > tee -a ./mri_nu_correct.mni.log > > Program nu_correct, built from: > > Package MNI N3, version 1.10, compiled by nicks@fishie > (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 > > if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$ > > if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745 > > set tmpdir = ./tmp.mri_nu_correct.mni.1745 > > mkdir -p $tmpdir > > mkdir -p ./tmp.mri_nu_correct.mni.1745 > > echo "tmpdir is $tmpdir" | tee -a $LF > > echo tmpdir is ./tmp.mri_nu_correct.mni.1745 > > tee -a ./mri_nu_correct.mni.log > > tmpdir is ./tmp.mri_nu_correct.mni.1745 > > set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc ) > > set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc ) > > if ( $UseFloat ) set cmd = ( $cmd -odt float ) > > if ( 1 ) set cmd = ( mri_convert orig.mgz > ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) > > set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc > -odt float ) > > pwd | & tee -a $LF > > pwd > > tee -a ./mri_nu_correct.mni.log > > /media/sf_Imagery/FreeSurfer/xx/mri > > echo $cmd | & tee -a $LF > > echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > tee -a ./mri_nu_correct.mni.log > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > $cmd | & tee -a $LF > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > tee -a ./mri_nu_correct.mni.log > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from orig.mgz... > > TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 > > i_ras = (-1, 1.49012e-08, 0) > > j_ras = (0, 0, -1) > > k_ras = (-1.30385e-08, 1, -5.96046e-08) > > changing data type from uchar to float (noscale = 0)... > > writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc... > > if ( $status ) then > > if ( 0 ) then > > @ nthIter = 1 ; > > @ nthIter = 1 > > while ( $nthIter < = $nIters ) > > while ( 1 < = 1 ) > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > echo "--------------------------------------------------------" | & > tee -a $LF > > echo -------------------------------------------------------- > > tee -a ./mri_nu_correct.mni.log > > -------------------------------------------------------- > > echo "Iteration $nthIter `date`" | & tee -a $LF > > echo Iteration 1 `date` > > tee -a ./mri_nu_correct.mni.log > > date > > Iteration 1 Mon Jun 23 15:32:49 EDT 2014 > > @ m = $nthIter - 1 > > @ m = 1 - 1 > > set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc > $tmpdir/nu${nthIter}.mnc ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) > > set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ; > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ ) > > if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ; > > if ( 1 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) > > if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ; > > if ( 0 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop ) > > if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ; > > if ( 1 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) > > if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ; > > if ( 0 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm ) > > echo $cmd | & tee -a $LF > > echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > tee -a ./mri_nu_correct.mni.log > > nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > $cmd | & tee -a $LF > > nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > tee -a ./mri_nu_correct.mni.log > > [fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] > [2014-06-23 15:32:49] running: > > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp > -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.imp > > Assertion failed at line 827 in file templates/CachedArray.cc > > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=256) > > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=256) > > if ( $status ) then > > if ( 0 ) then > > rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp > > rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu0.imp > > @ nthIter = $nthIter + 1 ; > > @ nthIter = 1 + 1 > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > end > > end > > while ( $nthIter < = $nIters ) > > while ( 2 < = 1 ) > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > set numnc = $tmpdir/nu$nIters.mnc > > set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc > > if ( $DoRescale ) then > > if ( 0 ) then > > if ( ! -e $numnc ) then > > if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then > > echo "ERROR: file $numnc does not exist!" | & tee -a $LF > > echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! > > tee -a ./mri_nu_correct.mni.log > > ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! > > exit 1 ; > > exit 1 > > ------------------------------------------------------------------------ > > This transmission, including any attachments, is for the sole use of > the intended recipient (s) and may contain information that is > confidential, proprietary, legally privileged, or otherwise protected > by law from disclosure. Any unauthorized review, use, copying, > disclosure, or distribution is prohibited. If you are not the intended > recipient, or the person responsible for delivering this to an > addressee, you should notify the sender immediately by telephone or by > reply e-mail, and destroy all copies of the original message. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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The problem is probably that your slice thickness is 5.2mm. This will certainly never work for getting surfaces, though I don't quite understand why nu is failing
doug
On 06/30/2014 03:51 PM, Remy Wahnoun wrote:
Thanks Douglas, orig.mgz looks fine to me. Do you know if there is any detailed log i could look into? Or maybe process tasks one after the other?
*Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University /www.NeuralControl.net http://www.NeuralControl.net/
On Wed, Jun 25, 2014 at 7:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz to see if that looks ok On 06/23/2014 03:58 PM, Remy Wahnoun wrote: > > Thanks Douglas, > > I definitely appreciate your help. > > Here is what it Spit out, > > *Rémy Wahnoun, PhD* > > Biomedical Research Group Manager > > Barrow Neurological Institute at Phoenix Children's Hospital > > Adjunct Faculty, Arizona State University > > /www.NeuralControl.net <http://www.NeuralControl.net> <http://www.neuralcontrol.net/>/ > > set echo = 1 ; > > set debug = 1 ; > > set debug = 1 > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 11 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --n > > shift > > switch ( $flag ) > > switch ( --n ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 10 == 0 ) goto arg1err > > set nIters = $argv[1] ; shift ; > > set nIters = 1 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 9 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --proto-iters > > shift > > switch ( $flag ) > > switch ( --proto-iters ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 8 == 0 ) goto arg1err > > set nProtoIters = $argv[1] ; shift ; > > set nProtoIters = 1000 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 7 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --distance > > shift > > switch ( $flag ) > > switch ( --distance ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 6 == 0 ) goto arg1err > > set Distance = $argv[1] ; shift ; > > set Distance = 50 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 5 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --no-rescale > > shift > > switch ( $flag ) > > switch ( --no-rescale ) > > set DoRescale = 0 ; > > set DoRescale = 0 > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 4 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --i > > shift > > switch ( $flag ) > > switch ( --i ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 3 == 0 ) goto arg1err > > set InVol = $argv[1] ; shift ; > > set InVol = orig.mgz > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 2 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --o > > shift > > switch ( $flag ) > > switch ( --o ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 1 == 0 ) goto arg1err > > set OutVol = $argv[1] ; shift ; > > set OutVol = orig_nu.mgz > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 0 != 0 ) > > goto parse_args_return ; > > goto parse_args_return > > goto check_params ; > > goto check_params > > if ( $#InVol == 0 ) then > > if ( 1 == 0 ) then > > if ( ! -e $InVol ) then > > if ( ! -e orig.mgz ) then > > if ( $#OutVol == 0 ) then > > if ( 1 == 0 ) then > > goto check_params_return ; > > goto check_params_return > > set OutDir = `dirname $OutVol` ; > > set OutDir = `dirname $OutVol` > > dirname orig_nu.mgz > > mkdir -p $OutDir ; > > mkdir -p . > > if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log > > if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log > > set LF = ./mri_nu_correct.mni.log > > if ( -e $LF ) mv $LF $LF.bak > > if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log > ./mri_nu_correct.mni.log.bak > > mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak > > pwd | tee -a $LF > > pwd > > tee -a ./mri_nu_correct.mni.log > > /media/sf_Imagery/FreeSurfer/xx/mri > > which mri_nu_correct.mni | tee -a $LF > > which mri_nu_correct.mni > > tee -a ./mri_nu_correct.mni.log > > /usr/local/freesurfer/bin/mri_nu_correct.mni > > echo $cmdargs | tee -a $LF > > echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i > orig.mgz --o orig_nu.mgz > > tee -a ./mri_nu_correct.mni.log > > --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i > orig.mgz --o orig_nu.mgz > > echo "nIters $nIters" | tee -a $LF > > echo nIters 1 > > tee -a ./mri_nu_correct.mni.log > > nIters 1 > > echo $VERSION | tee -a $LF > > tee -a ./mri_nu_correct.mni.log > > echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > > $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > > uname -a | tee -a $LF > > uname -a > > tee -a ./mri_nu_correct.mni.log > > Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 > 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux > > date | tee -a $LF > > date > > tee -a ./mri_nu_correct.mni.log > > Mon Jun 23 15:32:45 EDT 2014 > > nu_correct -version | tee -a $LF > > nu_correct -version > > tee -a ./mri_nu_correct.mni.log > > Program nu_correct, built from: > > Package MNI N3, version 1.10, compiled by nicks@fishie > (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 > > if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$ > > if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745 > > set tmpdir = ./tmp.mri_nu_correct.mni.1745 > > mkdir -p $tmpdir > > mkdir -p ./tmp.mri_nu_correct.mni.1745 > > echo "tmpdir is $tmpdir" | tee -a $LF > > echo tmpdir is ./tmp.mri_nu_correct.mni.1745 > > tee -a ./mri_nu_correct.mni.log > > tmpdir is ./tmp.mri_nu_correct.mni.1745 > > set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc ) > > set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc ) > > if ( $UseFloat ) set cmd = ( $cmd -odt float ) > > if ( 1 ) set cmd = ( mri_convert orig.mgz > ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) > > set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc > -odt float ) > > pwd | & tee -a $LF > > pwd > > tee -a ./mri_nu_correct.mni.log > > /media/sf_Imagery/FreeSurfer/xx/mri > > echo $cmd | & tee -a $LF > > echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > tee -a ./mri_nu_correct.mni.log > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > $cmd | & tee -a $LF > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > tee -a ./mri_nu_correct.mni.log > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from orig.mgz... > > TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 > > i_ras = (-1, 1.49012e-08, 0) > > j_ras = (0, 0, -1) > > k_ras = (-1.30385e-08, 1, -5.96046e-08) > > changing data type from uchar to float (noscale = 0)... > > writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc... > > if ( $status ) then > > if ( 0 ) then > > @ nthIter = 1 ; > > @ nthIter = 1 > > while ( $nthIter < = $nIters ) > > while ( 1 < = 1 ) > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > echo "--------------------------------------------------------" | & > tee -a $LF > > echo -------------------------------------------------------- > > tee -a ./mri_nu_correct.mni.log > > -------------------------------------------------------- > > echo "Iteration $nthIter `date`" | & tee -a $LF > > echo Iteration 1 `date` > > tee -a ./mri_nu_correct.mni.log > > date > > Iteration 1 Mon Jun 23 15:32:49 EDT 2014 > > @ m = $nthIter - 1 > > @ m = 1 - 1 > > set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc > $tmpdir/nu${nthIter}.mnc ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) > > set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ; > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ ) > > if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ; > > if ( 1 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) > > if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ; > > if ( 0 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop ) > > if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ; > > if ( 1 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) > > if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ; > > if ( 0 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm ) > > echo $cmd | & tee -a $LF > > echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > tee -a ./mri_nu_correct.mni.log > > nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > $cmd | & tee -a $LF > > nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > tee -a ./mri_nu_correct.mni.log > > [fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] > [2014-06-23 15:32:49] running: > > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp > -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.imp > > Assertion failed at line 827 in file templates/CachedArray.cc > > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=256) > > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=256) > > if ( $status ) then > > if ( 0 ) then > > rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp > > rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu0.imp > > @ nthIter = $nthIter + 1 ; > > @ nthIter = 1 + 1 > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > end > > end > > while ( $nthIter < = $nIters ) > > while ( 2 < = 1 ) > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > set numnc = $tmpdir/nu$nIters.mnc > > set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc > > if ( $DoRescale ) then > > if ( 0 ) then > > if ( ! -e $numnc ) then > > if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then > > echo "ERROR: file $numnc does not exist!" | & tee -a $LF > > echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! > > tee -a ./mri_nu_correct.mni.log > > ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! > > exit 1 ; > > exit 1 > > ------------------------------------------------------------------------ > > This transmission, including any attachments, is for the sole use of > the intended recipient (s) and may contain information that is > confidential, proprietary, legally privileged, or otherwise protected > by law from disclosure. 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Good afternoon, I tried again with a dataset from ieeg.org. This time, i'm starting with a 3T and i believe the thinckness is about 1mm. I do get a warning stating that my tcsh isnt up to date, and may return errors. Could it be that i didnt set up everything the right way? Sorry for the noob questions, i just started with freesurfer. Thanks in advance,
*Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net http://www.NeuralControl.net*
On Mon, Jul 7, 2014 at 9:42 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The problem is probably that your slice thickness is 5.2mm. This will certainly never work for getting surfaces, though I don't quite understand why nu is failing
doug
On 06/30/2014 03:51 PM, Remy Wahnoun wrote:
Thanks Douglas, orig.mgz looks fine to me. Do you know if there is any detailed log i could look into? Or maybe process tasks one after the other?
*Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University /www.NeuralControl.net http://www.NeuralControl.net/
On Wed, Jun 25, 2014 at 7:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz to see if that looks ok On 06/23/2014 03:58 PM, Remy Wahnoun wrote: > > Thanks Douglas, > > I definitely appreciate your help. > > Here is what it Spit out, > > *Rémy Wahnoun, PhD* > > Biomedical Research Group Manager > > Barrow Neurological Institute at Phoenix Children's Hospital > > Adjunct Faculty, Arizona State University > > /www.NeuralControl.net <http://www.NeuralControl.net> <http://www.neuralcontrol.net/>/ > > set echo = 1 ; > > set debug = 1 ; > > set debug = 1 > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 11 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --n > > shift > > switch ( $flag ) > > switch ( --n ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 10 == 0 ) goto arg1err > > set nIters = $argv[1] ; shift ; > > set nIters = 1 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 9 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --proto-iters > > shift > > switch ( $flag ) > > switch ( --proto-iters ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 8 == 0 ) goto arg1err > > set nProtoIters = $argv[1] ; shift ; > > set nProtoIters = 1000 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 7 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --distance > > shift > > switch ( $flag ) > > switch ( --distance ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 6 == 0 ) goto arg1err > > set Distance = $argv[1] ; shift ; > > set Distance = 50 > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 5 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --no-rescale > > shift > > switch ( $flag ) > > switch ( --no-rescale ) > > set DoRescale = 0 ; > > set DoRescale = 0 > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 4 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --i > > shift > > switch ( $flag ) > > switch ( --i ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 3 == 0 ) goto arg1err > > set InVol = $argv[1] ; shift ; > > set InVol = orig.mgz > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 2 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --o > > shift > > switch ( $flag ) > > switch ( --o ) > > if ( $#argv == 0 ) goto arg1err ; > > if ( 1 == 0 ) goto arg1err > > set OutVol = $argv[1] ; shift ; > > set OutVol = orig_nu.mgz > > shift > > breaksw > > breaksw > > end > > end > > while ( $#argv != 0 ) > > while ( 0 != 0 ) > > goto parse_args_return ; > > goto parse_args_return > > goto check_params ; > > goto check_params > > if ( $#InVol == 0 ) then > > if ( 1 == 0 ) then > > if ( ! -e $InVol ) then > > if ( ! -e orig.mgz ) then > > if ( $#OutVol == 0 ) then > > if ( 1 == 0 ) then > > goto check_params_return ; > > goto check_params_return > > set OutDir = `dirname $OutVol` ; > > set OutDir = `dirname $OutVol` > > dirname orig_nu.mgz > > mkdir -p $OutDir ; > > mkdir -p . > > if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log > > if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log > > set LF = ./mri_nu_correct.mni.log > > if ( -e $LF ) mv $LF $LF.bak > > if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log > ./mri_nu_correct.mni.log.bak > > mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak > > pwd | tee -a $LF > > pwd > > tee -a ./mri_nu_correct.mni.log > > /media/sf_Imagery/FreeSurfer/xx/mri > > which mri_nu_correct.mni | tee -a $LF > > which mri_nu_correct.mni > > tee -a ./mri_nu_correct.mni.log > > /usr/local/freesurfer/bin/mri_nu_correct.mni > > echo $cmdargs | tee -a $LF > > echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale--i
> orig.mgz --o orig_nu.mgz > > tee -a ./mri_nu_correct.mni.log > > --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i > orig.mgz --o orig_nu.mgz > > echo "nIters $nIters" | tee -a $LF > > echo nIters 1 > > tee -a ./mri_nu_correct.mni.log > > nIters 1 > > echo $VERSION | tee -a $LF > > tee -a ./mri_nu_correct.mni.log > > echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > > $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > > uname -a | tee -a $LF > > uname -a > > tee -a ./mri_nu_correct.mni.log > > Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 > 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux > > date | tee -a $LF > > date > > tee -a ./mri_nu_correct.mni.log > > Mon Jun 23 15:32:45 EDT 2014 > > nu_correct -version | tee -a $LF > > nu_correct -version > > tee -a ./mri_nu_correct.mni.log > > Program nu_correct, built from: > > Package MNI N3, version 1.10, compiled by nicks@fishie > (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 > > if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$ > > if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745 > > set tmpdir = ./tmp.mri_nu_correct.mni.1745 > > mkdir -p $tmpdir > > mkdir -p ./tmp.mri_nu_correct.mni.1745 > > echo "tmpdir is $tmpdir" | tee -a $LF > > echo tmpdir is ./tmp.mri_nu_correct.mni.1745 > > tee -a ./mri_nu_correct.mni.log > > tmpdir is ./tmp.mri_nu_correct.mni.1745 > > set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc ) > > set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc ) > > if ( $UseFloat ) set cmd = ( $cmd -odt float ) > > if ( 1 ) set cmd = ( mri_convert orig.mgz > ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) > > set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc > -odt float ) > > pwd | & tee -a $LF > > pwd > > tee -a ./mri_nu_correct.mni.log > > /media/sf_Imagery/FreeSurfer/xx/mri > > echo $cmd | & tee -a $LF > > echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > tee -a ./mri_nu_correct.mni.log > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > $cmd | & tee -a $LF > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > tee -a ./mri_nu_correct.mni.log > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from orig.mgz... > > TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 > > i_ras = (-1, 1.49012e-08, 0) > > j_ras = (0, 0, -1) > > k_ras = (-1.30385e-08, 1, -5.96046e-08) > > changing data type from uchar to float (noscale = 0)... > > writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc... > > if ( $status ) then > > if ( 0 ) then > > @ nthIter = 1 ; > > @ nthIter = 1 > > while ( $nthIter < = $nIters ) > > while ( 1 < = 1 ) > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > echo "--------------------------------------------------------" | & > tee -a $LF > > echo -------------------------------------------------------- > > tee -a ./mri_nu_correct.mni.log > > -------------------------------------------------------- > > echo "Iteration $nthIter `date`" | & tee -a $LF > > echo Iteration 1 `date` > > tee -a ./mri_nu_correct.mni.log > > date > > Iteration 1 Mon Jun 23 15:32:49 EDT 2014 > > @ m = $nthIter - 1 > > @ m = 1 - 1 > > set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc > $tmpdir/nu${nthIter}.mnc ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) > > set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ; > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ ) > > if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ; > > if ( 1 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) > > if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ; > > if ( 0 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop ) > > if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ; > > if ( 1 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) > > set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) > > if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ; > > if ( 0 ) set cmd = ( nu_correct -clobber > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm ) > > echo $cmd | & tee -a $LF > > echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > tee -a ./mri_nu_correct.mni.log > > nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > $cmd | & tee -a $LF > > nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 > > tee -a ./mri_nu_correct.mni.log > > [fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] > [2014-06-23 15:32:49] running: > > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4-auto_mask
> -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp > -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ > ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu1.imp > > Assertion failed at line 827 in file templates/CachedArray.cc > > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=256) > > nu_correct: crashed while running nu_estimate_np_and_em(termination
> status=256) > > if ( $status ) then > > if ( 0 ) then > > rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp > > rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc > ./tmp.mri_nu_correct.mni.1745/nu0.imp > > @ nthIter = $nthIter + 1 ; > > @ nthIter = 1 + 1 > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > end > > end > > while ( $nthIter < = $nIters ) > > while ( 2 < = 1 ) > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > echo " " | & tee -a $LF > > echo > > tee -a ./mri_nu_correct.mni.log > > set numnc = $tmpdir/nu$nIters.mnc > > set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc > > if ( $DoRescale ) then > > if ( 0 ) then > > if ( ! -e $numnc ) then > > if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then > > echo "ERROR: file $numnc does not exist!" | & tee -a $LF > > echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! > > tee -a ./mri_nu_correct.mni.log > > ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! > > exit 1 ; > > exit 1 > >
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